homi vs. homi

From ScienceDaily: Humans And Chimpanzees Genetically More Similar Than One Yeast Variety Is To Another

Scientists at the University of Gothenburg in Sweden say that humans and chimps are more similar on that level than two yeast species in the same genus. (FYI, we're in the same family as chimps, Hominidae or the great apes.)

I do think it's pretty cool... I like chimps, at least theoretically, as I don't know if I've ever met them. But they're cute, and they seem smart and feisty, and except for the whole endangered-species thing, I sometimes think I'd rather be an ape than a human.

I think this is a crappy comparison, though. This article says that there is a 4% difference in genes between the two yeast species, Saccharomyces cerevisiae and S. paradoxus, and a 1% difference between chimps and humans.

So, S. cerevisiae has 12,156,677 base pairs. I couldn't find a figure for the other. But say it's the same amount. With a 4% difference, that means around 486,267 base pairs are out of order or replaced in some way.

Not such an exact number for humans; everything says "approximately 3 billion." We can go with that, though. No numbers for the chimps, either, but you should look at the wiki article because they are adorable. Anyway. A 1% difference in 3 billion genes is... 3 million.

I just think there is a slight difference between almost 500,000 and 3 million, no matter the percentages.

Ah, well, I'm not a geneticist or anything. Maybe it is deep and meaningful. It is pretty cool to read about the Chimpanzee genome project and look at the only really obvious difference: at some point, for us, the 2nd and 3rd chromosomes that the chimp and human lines shared fused into one larger chromosome, with the addition about 150,000 or so base pairs. And since according to that article I posted this morning, the human and chimp line underwent the burst of genetic duplication that is thought to be the basis of our "human-ness," chimps are like our extended family, and I'm not trying to make a taxonomy pun here. They're like our cousin. Maybe second cousin, once removed. Hey, I don't mind grooming, but I won't eat mites.

now you see the true advantage of being third!

From ScienceDaily: Survival Of The Weakest? Cyclical Competition Of 3 Species Favors Weakest As Victor

An curious study from a German university about evolution, the idea of the survival of the fittest, and game theory. As we know, "these processes increase the 'fitness' of the species overall, since, of two competing species, only the fittest would survive." In simulations, researchers pitted three cyclically competitive species against one another, so that one species is weaker than the second, but stronger than the third. Sort of like rock-paper-scissors, only scissors can't be beaten by rock; rock's a weakling. Strangely, interestingly enough, the two strongest species kill each other off, and the third weaker species survives. Rock isn't weak; he's the Heir of Slytherin. Whether the differences in strength are large or small, the third species is the winner "with very high probability."

"The Survival of the fittest" as a metaphor for natural selection has allowed for a lot of interpretation, namely as the continuing triumph of the strong over the weak. A study like shows natural selection is not that pat. "Fittest" doesn't always mean strongest/smartest/fastest/sharpest. Leading the study was Prof. Erwin Frey, who says that this study "shows once more that chance plays a big part in the dynamics of an ecosystem."

Don't discount this just because it's a simulation, because Prof. Frey recalls, "Incidentally, in experiments that were conducted a couple of years ago on bacterial colonies, in order to study cyclical competition, there was one clear result: The weakest of the three species emerged victorious from the competition."

genetic "volcano"

From ScienceDaily: Did Burst Of Gene Duplication Set Stage For Human Evolution?

This is pretty crazy stuff. Around 10 million years ago, the common ancestor of chimpanzees and humans started undergoing gene duplication at a much faster rate than normal, while other mutations like a single nucleotide change became less prevalent.

Evan Eichler, a geneticist with the University of Washington says, "There's a big burst of activity that happens where genomes are suddenly rearranged and changed." Duplication slowed down after the chimp and human lines diverged. '"You might like to think that humans are special because we have more duplications than did earlier species," he says, "but that's not the case."'

Apparently, though, this crazy burst of duplication is what makes humans human. It "creat[ed] an instability that persists in the genome of modern humans and contributes to diseases like autism and schizophrenia. But that gene duplication also may be responsible for a genetic flexibility that has resulted in some uniquely human characteristics."

son of a cabbage

From COSMOS Magazine: Darwin at 200: The origin of a theory

COSMOS did a series this week on Charles Darwin, evolution, and the Galapagos in celebration of his 200th birthday. (I wonder if they did the stripper-in-the-cake thing, too?)

This particular article details the history of the idea and the theory beginning in 1699. It's an entertaining read. The best line:

"Jocular types greeted each other on the street with phrases like, 'Well, son of a cabbage, whither art thou progressing?'"

Ah, Victorians and their pop culture references.

you scratch my back...

From ScienceDaily: Small Male Chimps Use Politics, Rather Than Aggression, To Lead The Pack

Pretty interesting. Scientists observed a smaller chimp leader "obsessively groom[ing] both male and female chimpanzees to maintain his top position." They also observed a very large and aggressive leader as being a "stingy groomer."

just no genome compare and contrast essays, please

From ScienceDaily: New Computational Technique Allows Comparison Of Whole Genomes As Easily As Whole Books

Based on a word frequency technique used to compare and categorize texts, professor of chemistry at UC Berkley Sung-Hou Kim and a group of researchers have developed a method that allows the comparison of entire genomes of species. Up to this point, comparisons have only been done between exons, which are the sequences of DNA used by RNA to make proteins. They ran a comparison of 518 genomes; six were eukaryotes, two random, and the rest bacteria and archaea. The tool, the feature frequency profile (FFP) method, easily separated the examples into domains and fairly reliably into phyla and classes, "with some interesting discrepancies compared to the currently accepted groupings." Interestingly enough, "most" of those discrepancies involved species whose classifications are in dispute.

This sounds pretty amazing. Dr. Kim gives many fields where this method will help, but I think learning more about how species relate with each other is the most interesting thing. Previously I posted an article about how Darwin's Tree of Life doesn't really tell the whole story of evolution and the development of life. I can't wait to see what kind of awesome things they discover.

RNA is bi....directional?

From ScienceDaily: Rewrite the Textbooks: Transcription is Bidirectional

Scientists at the European Molecular Biology Lab in Germany have discovered that RNA transcription of DNA is bidirectional from promoters, as opposed to all transcription happening in one direction. DNA is still pretty mysterious, so even though this isn't as incredibly exciting as naked singularities or quantum communication, it's still good to know. Also, I can impress my biology professor. I like doing that.

a web, note a tree

From New Scientist: Why Darwin was wrong about the tree of life

Growing evidence is showing Darwin's idea of life as a growing, branching tree is too simple by spades, mostly because of RNA and DNA research. This article goes into detail about endosymbiosis and the development of eukaryotic cells, horizontal gene transfer, viable hybrids, and DNA implantation by viruses. There's even the discussion of the possibility that animals with distinct and completely different larvae and adult stages could be the descendants of two very different species. Very interesting.

dynamic evolution

From ScienceDaily: Evolutionary Process More Detailed Than Previously Believed, Study Shows

In observing yeast cells, scientists have realized that evolution doesn't happen in a straight line. The common model is that more useful mutations will disseminate through a population before developing further adaptations. However, Dr. Katy Kao at Texas A&M University and Dr. Gavin Sherlock at Stanford have realized that "evolutionary process [is] much more dynamic than initially thought." They witnessed separate yeast populations with different beneficial mutations compete with each other. One population that was almost eliminated for being less competitive was able mutate just in time to save itself.

Pretty interesting. With all those pictures of the lineage of species showing straight or forked lines, I definitely thought species moved as a whole or just eventually became other species. Now, it seems silly to think that there could only be one mutation at a time.

just like momma macaque

From ScienceDaily: Primate Culture Is Just a Stone's Throw Away From Human Evolution, Study Finds

I like it when animals are smarter than we think they are. Elephants self-recognizing, birds remembering if they've been spied stashing food, monkeys and apes using tools. And I think at least some animals feel. Maybe their emotions aren't as deep or varied as humans, but my cat gets jealous and feels content, and my dog gets lonely and becomes pleased.

According to this articles, scientists have been observing Japanese macaques for three decades. These monkeys... well, the article calls it "stone-handling," but considering it specifically describes them as "rubbing and clacking stones together, pounding them onto hard surfaces, picking them up, and cuddling, carrying, pushing, rolling and throwing them," I would just call it playing. And interestingly enough, researchers at the Primate Research Institute have found that mother macaques who play with stones more have children that spend more time with them, presumably because "the mothers' frequent stone-handling caught the infants' attention, and as a result, the infants acquired the behavior more quickly than other infants."

How cute. Baby monkeys want to be just like their parents.

Though I've read that a child's fascination for what adults and especially its parents are doing is coded in. Maybe that's why toy versions of adult equipment, like play stoves, are so popular. Pretty interesting stuff.

type 1 diabetes + celiac disease = bff

From ScienceDaily: Type 1 Diabetes And Celiac Disease Linked

"Richard A. Insel, MD., Executive Vice President, Research, at JDRF, said: "'These studies demonstrate that type 1 diabetes and celiac disease share far greater genetic overlap than had been appreciated, which helps explain the high prevalence of both diseases occurring simultaneously in an individual, and provide new avenues for understanding the cause and mechanisms of both diseases.'"

Apparently they found that people with these diseases share seven loci with each other, which is pretty crazy. I talked about this a few posts back, the correlation between these two diseases, but I thought it was only one gene that did it.

allergies: nature or nuture?

From the New York Times: Researchers Put a Microscope on Food Allergies

I find research like this pretty interesting, because 4/5 members of my immediate family have celiac disese, an allergy to certain types of grain proteins, especially in wheat, rye, barley, and oats. What causes allergies? Is it genetic or triggered by environment? My dad has it, and so do me and my two sisters. Recently I found out the same gene that can cause it has also been linked to thyroid disorders, which many of my mother's sisters have, and diabetes 1, which my grandmother had. So I wonder if my sisters and I got the gene from both sides, and that's why we have it.

A lot of people have wheat sensitivities, and I think a lot more people have celiac that don't realize it. Seems like autoimmune disorders are becoming more prevalent. I wonder if they're becoming more common, or just that we're noticing more?